She is now showing signs that all the touching and "niceness" between us the last few day is making her uncomfortable. She pulled away last night and this morning from back rubbing. I am immediately stopping any initiation of physical contact, which is really hard for me because even in the best of times, she never initiated so if I don't do it, it won't get done.
Another way to find out how to communicate love to her is to reflect back on how she used to communicate love to you. For example, you mentioned that she called you one day that she was buying jeans for you. Could "gift giving" be one of the ways she expresses her love? Then receiving gifts conveys "love" to her as well (Though at this stage, "gift giving" may be seen as "pursuit").
Does she see your physically touching her as meaning "you want sex"? When a relationship isn't fulfilling to a woman, or it's aggravating, her desire for sex with her partner can diminish and so she'd be guarded against seeming advances (even if they're not advances), rather than freely accepting them. Foreplay, they say, actually starts on Monday morning and continues throughout the week, with affirmations, compliments, being helpful with chores, really listening to her, being thoughtful and spending time together.